GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaQ in Phaeobacter inhibens BS107

Align RhaQ (characterized, see rationale)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein

Query= uniprot:Q7BSH2
         (337 letters)



>FitnessBrowser__Phaeo:GFF2762
          Length = 353

 Score =  145 bits (367), Expect = 1e-39
 Identities = 96/312 (30%), Positives = 157/312 (50%), Gaps = 9/312 (2%)

Query: 30  VLLFAVAVLIFVFNSLASPYFLDAWNLSDATFNFTEKAMIAFAMALLVISGEIDLSVAAI 89
           V L  + + + VF  L    F   + L+          ++A A +L++++  IDLSV AI
Sbjct: 43  VPLIVLVLSVIVFGLLLGSKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAI 102

Query: 90  IALASTAMGA-AVQIGIGTPGLVLIGIGTGLACGVFNGVLVSVLKLPSIVVTIGTMSLFR 148
           + L+S  MG    + G+     V  G+  G  CG  NG LV+ +KLP  +VT+G   +  
Sbjct: 103 MVLSSVVMGQFTFRYGLPPEVAVACGLICGTICGFINGWLVARMKLPPFIVTLGMWQIVL 162

Query: 149 GISYI-----VLGDQAYGKYPADFAYFGQGYVVW--VFSFEFVLFIVLAVLFAILLHATN 201
             +++      +  Q           FG+   +   VF++  +  ++L VL A +L  T 
Sbjct: 163 ASNFLYSANETIRSQTIAAEAPLLQLFGEKIKIGGAVFTYGVIFMVILVVLLAYVLRHTA 222

Query: 202 FGRQVYAIGNNDFAARFSGIPVERVKSILFLLTGIMSGIAAVCLTSRLGSTRPSIAQGWE 261
           +GR VYA+G++  AA  SG+ V RV   +++L+G++   A   +  R+GS  P+  Q   
Sbjct: 223 WGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGSVSPTSGQLAN 282

Query: 262 LEVVTMVVLGGISILGGFRHDRGVFVIAAFVMGLVTFGLGLLNLPGIVMSIFIGLLIIVT 321
           +E +T VV+GGIS+ GG     G F   A ++G+ T GL LL        + IGLLII  
Sbjct: 283 IESITAVVIGGISLFGGRGSILGTF-FGALIVGVFTLGLRLLGADAQWTYLLIGLLIIAA 341

Query: 322 IAIPIIARRIKL 333
           +A+    R++ +
Sbjct: 342 VAVDQWIRKVSV 353


Lambda     K      H
   0.330    0.145    0.423 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 355
Number of extensions: 27
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 337
Length of database: 353
Length adjustment: 29
Effective length of query: 308
Effective length of database: 324
Effective search space:    99792
Effective search space used:    99792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory